Age-Structured Disease Transmission Model with Interventions

;name agents
breed [young_ones young_one]
breed [young_adults young_adult]
breed [middle_aged_adults middle_aged_adult]
breed [seniors senior]

; variables that can be updated/changed as agents experience changes to themselves or the environment
globals [
  num-healthy
  num-infected
  num-recovered
  num-dead
  num-healthy-young-ones
  num-healthy-young-adults
  num-healthy-middle-aged-adults
  num-healthy-seniors
  num-infected-young-ones
  num-infected-young-adults
  num-infected-middle-aged-adults
  num-infected-seniors
  num-recovered-young-ones
  num-recovered-young-adults
  num-recovered-middle-aged-adults
  num-recovered-seniors
  num-dead-young-ones
  num-dead-young-adults
  num-dead-middle-aged-adults
  num-dead-seniors
  transmission-rate
  incubation-period
  symptomatic-period
  Log-data
  total-contact-rate
  contact-rate
]
; variable unique to each agents
turtles-own [
  healthy?
  infected?
  recovered?
  dead?
  susceptibility
  critical-illness-rate
  age-group
  days-infected
  days-since-symptoms
  daily-contacts
  vaccinated?
  wearing-mask?
  secondary-infections ; Note: variable to track secondary infections
]

to setup
  clear-all

  ;assign values to relevant global variables
  set transmission-rate 0.0089
  set incubation-period 122.4
  set symptomatic-period 240
  set Log-data []
  set total-contact-rate 0

  ; Note: let is used to create local variables that are used only within the current block of code.
  ; set number of agents as proportions of the total population
  let num-young-ones round (total-turtles * young-ones-proportion)
  let num-young-adults round (total-turtles * young-adults-proportion)
  let num-middle-aged-adults round (total-turtles * middle-aged-adults-proportion)
  let num-seniors round (total-turtles * seniors-proportion)

  ; create locations
  create-locations

  ; create agents, define name, set agent specific unique variables/properties
  create-turtles num-young-ones [
    set breed young_ones
    set age-group "young ones"
    set-turtle-properties young-ones-susceptibility young-ones-vaccination-rate young-ones-masking-rate young-ones-contact-rate
  ]
  create-turtles num-young-adults [
    set breed young_adults
    set age-group "young adults"
    set-turtle-properties young-adults-susceptibility young-adults-vaccination-rate young-adults-masking-rate young-adults-contact-rate
  ]
  create-turtles num-middle-aged-adults [
    set breed middle_aged_adults
    set age-group "middle aged adults"
    set-turtle-properties middle-aged-adults-susceptibility middle-aged-adults-vaccination-rate middle-aged-adults-masking-rate middle-aged-adults-contact-rate
  ]
  create-turtles num-seniors [
    set breed seniors
    set age-group "seniors"
    set-turtle-properties seniors-susceptibility seniors-vaccination-rate seniors-masking-rate seniors-contact-rate
  ]

  ;set number of intially infected
  repeat initial-infected [
    ask one-of turtles with [not infected?] [
      set infected? true
      set healthy? false
      set days-infected 0
      set color red
    ]
  ]

  reset-ticks
end 

; assign the unique variables to agents (boolean, integer, float)

to set-turtle-properties [initial-susceptibility vaccination-rate masking-rate initial-contact-rate]
  setxy random-xcor random-ycor
  set healthy? true
  set infected? false
  set recovered? false
  set dead? false
  set days-infected 0
  set days-since-symptoms 0
  set daily-contacts 0
  set vaccinated? (random-float 1 < vaccination-rate)
  set wearing-mask? (random-float 1 < masking-rate)
  set susceptibility initial-susceptibility
  set contact-rate initial-contact-rate
  set secondary-infections 0

  if vaccinated? [
    set susceptibility susceptibility * (1 - vaccination-effectiveness) ; Adjust susceptibility based on vaccination effectiveness
  ]

  if age-group = "young ones" [
    set critical-illness-rate 0.0004
    set color yellow
  ]
  if age-group = "young adults" [
    set critical-illness-rate 0.0029
    set color blue
  ]
  if age-group = "middle aged adults" [
    set critical-illness-rate 0.0039
    set color green
  ]
  if age-group = "seniors" [
    set critical-illness-rate 0.2
    set color violet
  ]
end 

to create-locations
  ask patches [
    if random-float 1 < 0.1 [set pcolor blue]
    if random-float 1 < 0.05 [set pcolor yellow]
    if random-float 1 < 0.03 [set pcolor orange]
    if random-float 1 < 0.05 [set pcolor green]
    if random-float 1 < 0.04 [set pcolor magenta]
    if random-float 1 < 0.02 [set pcolor black]
    if random-float 1 < 0.03 [set pcolor white]
  ]
end 
; define movement pattern based on states and age group

to move-to-location
  if infected? [
    if days-infected >= incubation-period [
      ifelse days-since-symptoms > 0 and days-since-symptoms <= symptomatic-period [
        ifelse random 2 = 0 [
          move-to one-of patches with [pcolor = magenta]
        ] [
          move-to one-of patches with [pcolor = black]
        ]
      ] [
        move-to one-of patches with [pcolor = magenta]
      ]
    ]
  ]
  if not infected? [
    let current-hour ticks mod 24
    let current-day (ticks / 24) mod 7


      ifelse current-day < 5 [
        if age-group = "young ones" [
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 15 [move-to one-of patches with [pcolor = orange]]
          if current-hour >= 15.5 and current-hour < 17 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 17 and current-hour < 18 [move-to one-of patches with [pcolor = orange]]
          if current-hour >= 18 and current-hour < 19 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19 and current-hour < 20 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 20 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "young adults" [
          if current-hour >= 7 and current-hour < 8 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 17 [move-to one-of patches with [pcolor = yellow]]
          if current-hour >= 17.5 and current-hour < 18.5 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 18.5 and current-hour < 19.5 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19.5 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 21 and current-hour < 22 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "middle aged adults" [
          if current-hour >= 6 and current-hour < 7 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 7 and current-hour < 8 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 8 and current-hour < 17 [move-to one-of patches with [pcolor = yellow]]
          if current-hour >= 17.5 and current-hour < 18.5 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18.5 and current-hour < 19.5 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19.5 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 21 and current-hour < 22 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "seniors" [
          if current-hour >= 7 and current-hour < 8 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 12 [move-to one-of patches with [pcolor = yellow]]
          if current-hour >= 12 and current-hour < 13 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 13 and current-hour < 15 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 15 and current-hour < 17 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 17 and current-hour < 18 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 18 and current-hour < 19 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "elderly" [
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 11 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 11 and current-hour < 13 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 13 and current-hour < 14 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 14 and current-hour < 16 [move-to one-of patches with [pcolor = white]]
          if current-hour >= 16 and current-hour < 18 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18 and current-hour < 19 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
        ]
      ] [
        if age-group = "young ones" [
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 11 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 11 and current-hour < 12 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 12 and current-hour < 13 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 13 and current-hour < 15 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 15 and current-hour < 17 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 17 and current-hour < 18 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18 and current-hour < 19 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19 and current-hour < 20 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 20 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "young adults" [
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 11 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 11 and current-hour < 13 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 13 and current-hour < 15 [move-to one-of patches with [pcolor = white]]
          if current-hour >= 15 and current-hour < 17 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 17 and current-hour < 18 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18 and current-hour < 20 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 20 and current-hour < 22 [move-to one-of patches with [pcolor = white]]
        ]
        if age-group = "middle aged adults" [
          if current-hour >= 7 and current-hour < 8 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 17 [move-to one-of patches with [pcolor = yellow]]
          if current-hour >= 17.5 and current-hour < 18.5 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18.5 and current-hour < 19.5 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19.5 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 21 and current-hour < 22 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "seniors" [
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 11 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 11 and current-hour < 13 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 13 and current-hour < 14 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 14 and current-hour < 16 [move-to one-of patches with [pcolor = white]]
          if current-hour >= 16 and current-hour < 18 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18 and current-hour < 19 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
        ]
        if age-group = "elderly" [
          if current-hour >= 8 and current-hour < 9 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 9 and current-hour < 11 [move-to one-of patches with [pcolor = green]]
          if current-hour >= 11 and current-hour < 13 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 13 and current-hour < 14 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 14 and current-hour < 16 [move-to one-of patches with [pcolor = white]]
          if current-hour >= 16 and current-hour < 18 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 18 and current-hour < 19 [move-to one-of patches with [pcolor = blue]]
          if current-hour >= 19 and current-hour < 21 [move-to one-of patches with [pcolor = blue]]
        ]
      ]
    ]
    setxy random-xcor random-ycor
end 

; define general movement pattern and behaviours

to go
  ask turtles [
    if not dead? [
      move-to-location
      infect-others
      develop-symptoms
      recover-or-die
    ]
  ]
  update-counts
  if num-infected = 0 [
    calculate-R0
    stop
  ]
  log-contact-rates
  tick
end 

to calculate-R0
  let total-secondary-infections sum [secondary-infections] of turtles with [infected? or recovered? or dead?]
  let total-infected count turtles with [infected? or recovered? or dead?]
  if total-infected > 0 [
    let R0 total-secondary-infections / total-infected
    print (word "R0: " R0)
  ]
end 

; define how infected agents spread the disease

to infect-others
  if infected? [
    ;define infectious period
    let infectious-start incubation-period - 24
    let infectious-end incubation-period + symptomatic-period + 72

    ;check if within infected period and define infection radius
    if days-infected >= infectious-start and days-infected <= infectious-end [
      let infection-radius 1
     ;if practicing-social-distancing? [
      ;  set infection-radius 0.2
     ; ]

      ;define set number and "condition" of likely to be infected
      let nearby-turtles turtles in-radius infection-radius with [not dead? and not infected?]
      ask n-of (count nearby-turtles * contact-rate) nearby-turtles [
        let adjusted-transmission-rate transmission-rate
        if wearing-mask? [
          set adjusted-transmission-rate transmission-rate * (1 - masking-effectiveness)
        ]
        ; if radom-float < adjusted-transmission-rate * susceptibility, get infected.
        if random-float 1 < adjusted-transmission-rate * susceptibility [
          set infected? true
          set healthy? false
          set days-infected 0
          set color red
          ask myself [set secondary-infections secondary-infections + 1]
        ]

        ; keep track of conatacts
        set daily-contacts daily-contacts + 1
        ask myself [set daily-contacts daily-contacts + 1]
      ]
    ]
  ]
end 

; define when infections should start, it will indicate when infected agents should isolate themselves

to develop-symptoms
  if infected? [
    if days-infected = incubation-period [
      set days-since-symptoms 0
    ]
    set days-since-symptoms days-since-symptoms + 1
  ]
end 

; define conditions for recovery or death

to recover-or-die
  if infected? [
    set days-infected days-infected + 1

    if days-infected > incubation-period [
      set days-since-symptoms days-since-symptoms + 1
    ]

    if days-since-symptoms >= symptomatic-period [
      if random-float 1 < critical-illness-rate [
        ifelse random-float 1 < 0.5 [
          set dead? true
          set infected? false
          set healthy? false
          set recovered? false
          set color black
        ] [
          set recovered? true
          set infected? false
          set healthy? false
          set dead? false
          set color gray
        ]
      ]

      ;fail safe to ensure that all agents that didnt die, did recover.
      if not dead? [
        set recovered? true
        set infected? false
        set healthy? false
        set dead? false
        set color gray
      ]
    ]

    ;recover after the symptomatic period has passed
    if days-infected > incubation-period + symptomatic-period [
      set recovered? true
      set infected? false
      set healthy? false
      set dead? false
      set color gray
    ]
  ]
end 

;update counts

to update-counts
  set num-healthy count turtles with [healthy?]
  set num-infected count turtles with [infected?]
  set num-recovered count turtles with [recovered?]
  set num-dead count turtles with [dead?]

  set num-healthy-young-ones count young_ones with [healthy?]
  set num-healthy-young-adults count young_adults with [healthy?]
  set num-healthy-middle-aged-adults count middle_aged_adults with [healthy?]
  set num-healthy-seniors count seniors with [healthy?]

  set num-infected-young-ones count young_ones with [infected?]
  set num-infected-young-adults count young_adults with [infected?]
  set num-infected-middle-aged-adults count middle_aged_adults with [infected?]
  set num-infected-seniors count seniors with [infected?]

  set num-recovered-young-ones count young_ones with [recovered?]
  set num-recovered-young-adults count young_adults with [recovered?]
  set num-recovered-middle-aged-adults count middle_aged_adults with [recovered?]
  set num-recovered-seniors count seniors with [recovered?]

  set num-dead-young-ones count young_ones with [dead?]
  set num-dead-young-adults count young_adults with [dead?]
  set num-dead-middle-aged-adults count middle_aged_adults with [dead?]
  set num-dead-seniors count seniors with [dead?]

  ;optional, can be replaced with output from behaviour space
  set Log-data lput (list ticks num-healthy num-infected num-recovered num-dead
              num-healthy-young-ones num-healthy-young-adults num-healthy-middle-aged-adults num-healthy-seniors
              num-infected-young-ones num-infected-young-adults num-infected-middle-aged-adults num-infected-seniors
              num-recovered-young-ones num-recovered-young-adults num-recovered-middle-aged-adults num-recovered-seniors
              num-dead-young-ones num-dead-young-adults num-dead-middle-aged-adults num-dead-seniors) Log-data
end 

to log-contact-rates
  let total-contacts sum [daily-contacts] of turtles
  set total-contact-rate total-contacts
  ask turtles [set daily-contacts 0]
end